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Architecture of RNA–RNA interactions
Current Opinion in Genetics & Development, 2022RNA molecules tend to form intricate tertiary structures via intramolecular RNA-RNA interactions (RRIs) to regulate transcription, RNA processing, and translation processes. In these biological processes, RNAs, especially noncoding RNAs, usually achieve their regulatory specificity through intermolecular RNA-RNA base pairing and execute their ...
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DYNAMIC RNA-RNA INTERACTIONS IN THE SPLICEOSOME
Annual Review of Genetics, 1994SUBSTRATE INTERACTIONS . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Ul snRNA-Intron Base-Pairing Interactions: Defining the Splice Sites . . . ... . .. .. 4 U6-5' Splice Site Base-Pairing: Double Recognition of the 5' Splice Site ..... .... 6 Base-Pairing with U2 snRNA Defines the Intron Branchpoint .. ..
H D, Madhani, C, Guthrie
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Web Services for RNA-RNA Interaction Prediction
2023Non-coding RNAs have various biological functions such as translational regulation, and RNA-RNA interactions play essential roles in the mechanisms of action of these RNAs. Therefore, RNA-RNA interaction prediction is an important problem in bioinformatics, and many tools have been developed for the computational prediction of RNA-RNA interactions.
Tsukasa, Fukunaga +2 more
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A heuristic approach to RNA–RNA interaction prediction
Journal of Theoretical Biology, 2012RNA-RNA interaction is used in many biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. In this regard, some algorithms have been formed to predict the structure of the interaction between two RNA molecules.
Montaseri, Soheila +2 more
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A grammatical approach to RNA–RNA interaction prediction
Pattern Recognition, 2009zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki
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Predicting novel RNA–RNA interactions
Current Opinion in Structural Biology, 2008The purpose of this article is to give a brief, yet concise overview of the current computational methods for predicting novel RNA-RNA interactions, that is interactions whose characteristic features we do not yet know. We start by briefly reviewing experimentally confirmed examples of RNA-RNA interactions before introducing computational methods for ...
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On the Approximation of Optimal Structures for RNA-RNA Interaction
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009The interaction of two RNA molecules is a common mechanism for many biological processes. Small interfering RNAs represent a simple example of such an interaction. But other more elaborate instances of RNA-RNA interaction exist. Therefore, algorithms that predict the structure of the RNA complex thus formed are of great interest.
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On RNA–RNA interaction structures of fixed topological genus
Mathematical Biosciences, 2015Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and a linear time uniform sampling algorithm for RNA complexes of fixed topological genus.
Fu, Benjamin Mingming +2 more
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Single Molecule Studies of RNA–RNA Interactions
2014Non-coding RNAs including microRNAs, siRNAs, and snoRNAs interact with their targets directly through RNA-RNA interactions by base-paring (van Himbergen et al., Nucleic Acids Res 21(8):1713-1717, 1993). RNA-RNA interactions play important roles in gene transcription and protein translation, which can be investigated with several experimental techniques
Dongmei, Yu +2 more
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Predicting RNA–RNA Interactions Using RNAstructure
2016RNA-RNA binding is a required step for many regulatory and catalytic processes in the cell. Identifying RNA-RNA hybridization sites is challenging because of the competition between intramolecular and intermolecular structure formation. A complete picture of RNA-RNA binding includes an understanding of single-stranded folding and binding site ...
Laura, DiChiacchio, David H, Mathews
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